GapMind for catabolism of small carbon sources

 

Protein WP_033099889.1 in Thermoactinomyces daqus H-18

Annotation: NCBI__GCF_000763315.1:WP_033099889.1

Length: 474 amino acids

Source: GCF_000763315.1 in NCBI

Candidate for 48 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism gabD hi Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 (characterized) 58% 100% 553.5
L-citrulline catabolism gabD hi Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 (characterized) 58% 100% 553.5
putrescine catabolism gabD hi Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 (characterized) 58% 100% 553.5
L-arginine catabolism davD med glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 55% 98% 523.1 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
L-citrulline catabolism davD med glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 55% 98% 523.1 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
L-lysine catabolism davD med glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 55% 98% 523.1 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
L-proline catabolism davD med glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized) 55% 98% 523.1 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
4-hydroxybenzoate catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 52% 92% 496.5 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
2'-deoxyinosine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 52% 92% 496.5 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
2-deoxy-D-ribose catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 52% 92% 496.5 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
ethanol catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 52% 92% 496.5 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
L-threonine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 52% 92% 496.5 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
thymidine catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 52% 92% 496.5 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
L-tryptophan catabolism adh med aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized) 52% 92% 496.5 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
L-arabinose catabolism xacF med Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 42% 98% 369.4 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
D-galacturonate catabolism dopDH med Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 42% 98% 369.4 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
D-glucuronate catabolism dopDH med Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 42% 98% 369.4 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
D-xylose catabolism dopDH med Alpha-ketoglutaric semialdehyde dehydrogenase 1; alphaKGSA dehydrogenase 1; 2,5-dioxovalerate dehydrogenase 1; 2-oxoglutarate semialdehyde dehydrogenase 1; KGSADH-I; Succinate-semialdehyde dehydrogenase [NAD(+)]; SSDH; EC 1.2.1.26; EC 1.2.1.24 (characterized) 42% 98% 369.4 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
L-arginine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 41% 94% 347.4 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
L-citrulline catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 41% 94% 347.4 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
putrescine catabolism patD med aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized) 41% 94% 347.4 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
L-phenylalanine catabolism pad-dh med Phenylacetaldehyde dehydrogenase; PAD; EC 1.2.1.39 (characterized) 40% 94% 345.9 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
L-arabinose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 37% 99% 326.2 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
L-fucose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 37% 99% 326.2 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
L-rhamnose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 37% 99% 326.2 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
L-threonine catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 37% 99% 326.2 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
D-xylose catabolism aldA lo lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized) 37% 99% 326.2 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
4-hydroxybenzoate catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 39% 97% 322 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
L-tryptophan catabolism praB lo 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized) 39% 97% 322 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
L-arginine catabolism kauB lo gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized) 37% 95% 306.2 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
L-arginine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 38% 96% 306.2 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
L-citrulline catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 38% 96% 306.2 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
putrescine catabolism puuC lo 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized) 38% 96% 306.2 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
L-isoleucine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 93% 290.4 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
myo-inositol catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 93% 290.4 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
propionate catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 93% 290.4 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
L-threonine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 93% 290.4 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
L-valine catabolism iolA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 93% 290.4 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
L-valine catabolism mmsA lo methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized) 34% 93% 290.4 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
L-tryptophan catabolism nbaE lo aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized) 36% 95% 275.8 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
L-arginine catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 34% 92% 257.7 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
L-arginine catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 34% 92% 257.7 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
L-citrulline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 34% 92% 257.7 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
L-citrulline catabolism rocA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 34% 92% 257.7 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
L-proline catabolism putA lo L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized) 34% 92% 257.7 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
L-arginine catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized) 34% 93% 219.5 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
L-citrulline catabolism astD lo N-succinylglutamate 5-semialdehyde dehydrogenase; Succinylglutamic semialdehyde dehydrogenase; SGSD; EC 1.2.1.71 (characterized) 34% 93% 219.5 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5
L-lysine catabolism amaB lo L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale) 32% 90% 215.3 Succinate-semialdehyde dehydrogenase [NADP(+)]; SSDH; EC 1.2.1.79 58% 553.5

Sequence Analysis Tools

View WP_033099889.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MHPDKMYINGRWIDAINKIDVINPATKKIIGSVPNGGATEAKMAVEAAYPAFQKWSKQPA
EERGKLLMKWFDLIEKHKDELAEIMTLEQGKPLQEARGEITYANSFISWYAEEGKRIYGE
TIPASSPDKRIFVQKQPVGVIAAITPWNFPAAMITRKVAPALAAGCTVVLKPSEETPFTA
LKLAELADQAGIPNGVLNVVTGDAESIANAWQKDSRVRKLTFTGSTPVGKILMRGAADTV
KKISLELGGHAPLIVTAQADIDKAVDGAIASKFRNAGQTCICTNRILADESIAEEFTVKL
AEKAAKLKVGNGLEESTDIGPLINEEAVKKVIKHIEDAKQKGGRVLTGGNRLTNQKGYFI
EPTVIANAKDDMLCMVEETFGPLIPVATFKTIDEAIERANNSSYGLAAYVYTENLREAVY
ISEALEYGIVGVNDGAPSAAQAPFGGFKESGLGREGSRYGIEEFLEIKYISLGL

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory